add scale bars to zoom window

config.py

@@ -18,8 +18,6 @@
 UI_MIN_WIDTH = 1000
 UI_MIN_HEIGHT = 1000
 
-INITIAL_R = 1
-
 TILES_VERSION = 1
 
 PIEZO_UM_PER_LSB= 0.0058812 # from empirical measurements

schema.py

@@ -28,23 +28,28 @@ class Schema():
     LAPLACIAN_WINDOW = None
     FILTER_WINDOW = None
     NOM_STEP = None
+    SCALE_BAR_WIDTH_UM = None
+    INITIAL_R = 1
     @staticmethod
     def set_mag(mag):
         if mag == 20:
             Schema.PIX_PER_UM = PIX_PER_UM_20X
             Schema.LAPLACIAN_WINDOW = LAPLACIAN_WINDOW_20X
             Schema.NOM_STEP = NOM_STEP_20x
             Schema.FILTER_WINDOW = FILTER_WINDOW_20X
+            Schema.SCALE_BAR_WIDTH_UM = 5.0
         elif mag == 5:
             Schema.PIX_PER_UM = PIX_PER_UM_5X
             Schema.LAPLACIAN_WINDOW = LAPLACIAN_WINDOW_5X
             Schema.NOM_STEP = NOM_STEP_5x
             Schema.FILTER_WINDOW = FILTER_WINDOW_5X
+            Schema.SCALE_BAR_WIDTH_UM = 20.0
         elif mag == 10:
             Schema.PIX_PER_UM = PIX_PER_UM_10X
             Schema.LAPLACIAN_WINDOW = LAPLACIAN_WINDOW_10X
             Schema.NOM_STEP = NOM_STEP_10x
             Schema.FILTER_WINDOW = FILTER_WINDOW_10X
+            Schema.SCALE_BAR_WIDTH_UM = 10.0
         else:
             logging.error(f"Unhandled magnification parameter: {mag}")
     @staticmethod
@@ -53,6 +58,9 @@ def set_laplacian(value):
     @staticmethod
     def set_filter(value):
         Schema.FILTER_WINDOW = value
+    @staticmethod
+    def set_initial_r(value):
+        Schema.INITIAL_R = value
 
     def __init__(self, use_cache=True):
         self.schema = {

stitch.py

@@ -18,8 +18,6 @@
 from utils import *
 from config import *
 
-SCALE_BAR_WIDTH_UM = None
-
 # TODO:
 # - colorize the preview based on deviation from plane (triggered by button)
 # - make a "heat map" for MSE post-autostitch? (triggered by button)
@@ -70,7 +68,7 @@ def check_thumbnails(args):
 
     # Load based on filenames, and finalize the overall area
     for file in files:
-        if '_r' + str(INITIAL_R) in file.stem: # filter image revs by the initial default rev
+        if '_r' + str(Schema.INITIAL_R) in file.stem: # filter image revs by the initial default rev
             if force_generate or not (thumb_path / file.name).is_file:
                 img = cv2.imread(str(file), cv2.IMREAD_GRAYSCALE)
                 thumb = cv2.resize(img, None, None, fx=THUMB_SCALE, fy=THUMB_SCALE)
@@ -82,11 +80,11 @@ class MainWindow(QMainWindow):
     from mse_stitch import stitch_one_mse
     from template_stitch import stitch_one_template, stitch_auto_template_linear, restitch_one
     from blend import blend
-    from zoom import update_zoom_window, on_cv_zoom, get_centered_and_scaled_image
+    from zoom import update_zoom_window, on_cv_zoom, get_centered_and_scaled_image, draw_scale_bar
     from overview import redraw_overview, rescale_overview, update_selected_rect,\
         centroid_to_tile_bounding_rect_mm, snap_range, check_res_bounds,\
         pix_to_um_absolute, um_to_pix_absolute, preview_selection, get_coords_in_range,\
-        compute_selection_overlay, draw_rect_at_center, rect_at_center, on_focus_visualize
+        compute_selection_overlay, draw_rect_at_center, rect_at_center, on_focus_visualize, generate_fullres_overview
 
     def __init__(self):
         super().__init__()
@@ -358,7 +356,7 @@ def new_schema(self, args):
 
         # Load based on filenames, and finalize the overall area
         for file in files:
-            if '_r' + str(INITIAL_R) in file.stem: # filter image revs by the initial default rev
+            if '_r' + str(Schema.INITIAL_R) in file.stem: # filter image revs by the initial default rev
                 self.schema.add_tile(file, max_x = args.max_x, max_y = args.max_y)
         self.schema.finalize()
         self.schema.set_undo_checkpoint()
@@ -460,19 +458,8 @@ def main():
         raise ValueError('Invalid log level: %s' % args.loglevel)
     logging.basicConfig(level=numeric_level)
 
-    global SCALE_BAR_WIDTH_UM
-    if args.mag == 20:
-        SCALE_BAR_WIDTH_UM = 5.0
-    elif args.mag == 5:
-        SCALE_BAR_WIDTH_UM = 20.0
-    elif args.mag == 10:
-        SCALE_BAR_WIDTH_UM = 10.0
-    else:
-        logging.error("Magnification parameters not defined")
-        exit(0)
-    global INITIAL_R
-    INITIAL_R = args.initial_r
     Schema.set_mag(args.mag) # this must be called before we create the main window, so that the filter/laplacian values are correct by default
+    Schema.set_initial_r(args.initial_r)
 
     if False: # run unit tests
         from prims import Rect

zoom.py

@@ -3,6 +3,7 @@
 from schema import Schema
 import logging
 from prims import Rect, Point
+from config import *
 
 WINDOW_SIZE_X = 2000
 WINDOW_SIZE_Y = 2000
@@ -16,12 +17,14 @@ def on_cv_zoom(self, raw_value):
         self.zoom_scale = ((1.0 - 0.1) / (20 - 0)) * raw_value + 0.1
 
     img = self.get_centered_and_scaled_image()
-    cv2.imshow('zoom', cv2.resize(img, None, None, self.zoom_scale, self.zoom_scale))
+    rescaled = cv2.resize(img, None, None, self.zoom_scale, self.zoom_scale)
+    self.draw_scale_bar(rescaled)
+    cv2.imshow('zoom', rescaled)
 
 def get_centered_and_scaled_image(self):
     # ensure that the fullres dataset is pulled in. Warning: could take a while.
     if self.overview_fullres is None:
-        self.redraw_overview(blend=False, force_full_res=True)
+        self.generate_fullres_overview(blend=False)
 
     (x_c, y_c) = self.um_to_pix_absolute(self.roi_center_ums)
     # scale of 2.0 means we are zooming in by 2x; 0.5 means we are zooming out by 2x
@@ -48,7 +51,31 @@ def get_centered_and_scaled_image(self):
 
 def update_zoom_window(self):
     img = self.get_centered_and_scaled_image()
-    cv2.imshow('zoom', cv2.resize(img, None, None, self.zoom_scale, self.zoom_scale))
+    rescaled = cv2.resize(img, None, None, self.zoom_scale, self.zoom_scale)
+    self.draw_scale_bar(rescaled)
+    cv2.imshow('zoom', rescaled)
     if not self.trackbar_created:
         cv2.createTrackbar('scale', 'zoom', 20, 100, self.on_cv_zoom)
         self.trackbar_created = True
+
+def draw_scale_bar(self, img):
+    base_width = Schema.SCALE_BAR_WIDTH_UM
+    scale_adjusted_width = base_width / self.zoom_scale
+    # draw scale bar
+    cv2.rectangle(
+        img,
+        (50, 50),
+        (int(50 + scale_adjusted_width * (Schema.PIX_PER_UM * self.zoom_scale)), 60),
+        (255, 255, 255),
+        thickness = 1,
+        lineType = cv2.LINE_4,
+    )
+    cv2.putText(
+        img,
+        f"{scale_adjusted_width:0.1f} um",
+        (50, 45),
+        cv2.FONT_HERSHEY_SIMPLEX,
+        0.5,
+        (255, 255, 255),
+        bottomLeftOrigin=False
+    )